LAMMPS (18 Feb 2013)
# Simple rigid body system

units		lj
atom_style	atomic

pair_style	lj/cut 2.5

read_data	data.rigid
  orthogonal box = (-12 -12 -12) to (12 12 12)
  1 by 2 by 2 MPI processor grid
  81 atoms

velocity 	all create 100.0 4928459

# unconnected bodies

#group		clump1 id <> 1 9
#group		clump2 id <> 10 18
#group		clump3 id <> 19 27
#group		clump4 id <> 28 36
#group		clump5 id <> 37 45
#group		clump6 id <> 46 54
#group		clump7 id <> 55 63
#group		clump8 id <> 64 72
#group		clump9 id <> 73 81

#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 #	  	      clump6 clump7 clump8 clump9

# 1 chain of connected bodies

#group		clump1 id <> 1 9
#group		clump2 id <> 9 18
#group		clump3 id <> 18 27
#group		clump4 id <> 27 36
#group		clump5 id <> 36 45
#group		clump6 id <> 45 54
#group		clump7 id <> 54 63
#group		clump8 id <> 63 72
#group		clump9 id <> 72 81

#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 #	  	      clump6 clump7 clump8 clump9

# 2 chains of connected bodies

group		clump1 id <> 1 9
9 atoms in group clump1
group		clump2 id <> 9 18
10 atoms in group clump2
group		clump3 id <> 18 27
10 atoms in group clump3
group		clump4 id <> 27 36
10 atoms in group clump4
group		clump5 id <> 37 45
9 atoms in group clump5
group		clump6 id <> 45 54
10 atoms in group clump6
group		clump7 id <> 54 63
10 atoms in group clump7
group		clump8 id <> 63 72
10 atoms in group clump8
group		clump9 id <> 72 81
10 atoms in group clump9

fix 1 all poems group clump1 clump2 clump3 clump4
1 clusters, 4 bodies, 3 joints, 36 atoms
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
1 clusters, 5 bodies, 4 joints, 45 atoms

neigh_modify	exclude group clump1 clump1
neigh_modify	exclude group clump2 clump2
neigh_modify	exclude group clump3 clump3
neigh_modify	exclude group clump4 clump4
neigh_modify	exclude group clump5 clump5
neigh_modify	exclude group clump6 clump6
neigh_modify	exclude group clump7 clump7
neigh_modify	exclude group clump8 clump8
neigh_modify	exclude group clump9 clump9

thermo		100

#dump		1 all atom 50 dump.rigid.poems2

#dump		1 all image 100 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30
#dump_modify	1 pad 5

timestep 	0.0001
thermo		50
run		10000
WARNING: More than one fix poems (fix_poems.cpp:332)
WARNING: More than one fix poems (fix_poems.cpp:332)
WARNING: One or more atoms are time integrated more than once (modify.cpp:220)
Memory usage per processor = 2.24916 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0    196.00047    3632.2347            0    3668.5311   -2.7403788 
      50    12167.633    1505.5478            0    3758.8133    35.125973 
     100    17556.978    512.66277            0    3763.9549    11.137534 
     150    19579.586    138.04942            0    3763.8987   -29.953971 
     200     19757.51    105.30542            0    3764.1036 -0.030645317 
     250    18218.374    390.10747            0    3763.8804    13.711001 
     300    19383.039    174.40688            0    3763.8586    5.7240693 
     350    20125.986    36.972611            0    3764.0071    1.9559205 
     400    18888.816    266.10975            0    3764.0386    9.6362168 
     450    19307.656     188.2511            0     3763.743    1.9326206 
     500    16331.197    738.56392            0    3762.8597    9.1715579 
     550    19318.722    186.16172            0    3763.7027    3.0115336 
     600    19455.268    161.20621            0    3764.0336   0.55208034 
     650    18487.011    340.03216            0    3763.5528   -8.0359122 
     700    17321.201    556.32471            0    3763.9545   -13.631751 
     750    18979.187    249.04389            0    3763.7082   -2.6072455 
     800    19342.456    181.85552            0    3763.7918    8.1918726 
     850    19070.641    232.19342            0    3763.7936    7.3148472 
     900    19478.873    156.65987            0    3763.8586    2.4284987 
     950    19912.415    76.437437            0    3763.9216   -1.4667227 
    1000    16003.749    802.39753            0    3766.0548    46.642188 
    1050    19859.583     86.64176            0    3764.3424   -2.1961943 
    1100    19229.575    203.61488            0    3764.6473   -10.632365 
    1150      18821.6    279.15861            0      3764.64  -0.89495035 
    1200    19392.695    173.59744            0    3764.8373    1.8508753 
    1250    16459.624    717.32104            0    3765.3995    33.478127 
    1300    19343.863    182.59043            0    3764.7874   0.75890736 
    1350    20019.643    57.503573            0    3764.8448   0.31444671 
    1400    18549.582    329.31436            0    3764.4221    10.738303 
    1450    15163.926    957.47586            0    3765.6103    -17.92346 
    1500    19223.687    204.15182            0    3764.0939    -1.613452 
    1550    18147.996    404.12678            0    3764.8668    8.4194792 
    1600    18615.043    317.42471            0    3764.6548   -2.3288881 
    1650    20120.654    38.887882            0     3764.935   -8.7620352 
    1700    19450.908    162.98242            0    3765.0025    2.3254787 
    1750     19374.63    177.37994            0    3765.2744    8.9328764 
    1800    19424.404    167.93955            0    3765.0514  0.081221207 
    1850    17936.104     442.8692            0    3764.3699    6.6014634 
    1900    19982.594    64.406495            0    3764.8868   -2.9529141 
    1950    16215.626    761.95548            0    3764.8491    13.995806 
    2000    18584.494    322.10724            0    3763.6801    7.1652003 
    2050    20107.964    41.026031            0     3764.723  -0.31084595 
    2100    20002.303    60.598606            0    3764.7288   -6.7920431 
    2150     16950.12    626.52975            0    3765.4408    3.5077027 
    2200    20010.956    58.807784            0    3764.5404   -10.861982 
    2250    18982.743    247.00649            0    3762.3293  -0.53838506 
    2300    18401.159    354.90522            0    3762.5273    1.0923853 
    2350    19390.592    172.92882            0    3763.7792   -3.3521232 
    2400    16078.693    786.77936            0    3764.3151   -16.207246 
    2450    18869.645    268.89132            0      3763.27    11.210758 
    2500    19689.703    117.31993            0    3763.5612    4.3700595 
    2550    18867.605    269.38371            0    3763.3847    -5.673697 
    2600    17024.852    610.68855            0    3763.4389    6.2927269 
    2650    18723.802    296.52976            0    3763.9005    2.4475504 
    2700    19752.355    105.40597            0    3763.2494  -0.38635488 
    2750    19524.414    147.78984            0    3763.4221   -1.5733395 
    2800    17840.968     459.3254            0    3763.2085    29.661669 
    2850     18887.52    265.43414            0    3763.1231    3.7534553 
    2900    20160.325     29.79531            0    3763.1888    2.8076367 
    2950    17931.673    442.25832            0    3762.9386    4.1038365 
    3000    19003.992    243.57426            0     3762.832    3.5213285 
    3050    18907.933    261.70341            0    3763.1725    6.1845639 
    3100    19086.668    229.05632            0    3763.6245   -1.7059047 
    3150    19524.328    148.10446            0    3763.7208   -13.257029 
    3200    19888.015    80.720451            0    3763.6863   -5.9850932 
    3250    18329.653    367.80596            0    3762.1862    2.5356842 
    3300    17774.857    472.07926            0    3763.7194     26.05786 
    3350     18586.91    322.11111            0    3764.1316    5.7227572 
    3400    18142.722    404.27409            0    3764.0373    22.972948 
    3450    19641.028      126.721            0    3763.9484    4.4124099 
    3500    19716.345    112.83226            0    3764.0073    3.0970704 
    3550    19750.966     106.4596            0    3764.0458   -1.2020093 
    3600    19385.115    174.22116            0    3764.0572  -0.30312978 
    3650    19806.188    96.296016            0    3764.1086    1.3884533 
    3700    19632.503     128.4744            0    3764.1231    5.4783086 
    3750    19984.029     63.34637            0    3764.0924   -7.6169503 
    3800    19391.726    173.11834            0    3764.1788   -5.5199774 
    3850    19701.864     115.6328            0    3764.1262    -4.613059 
    3900    19071.277    232.53842            0    3764.2563   0.60414949 
    3950    19543.806    144.70463            0    3763.9279    3.9673805 
    4000    17072.153    601.63639            0    3763.1462    14.038181 
    4050    19472.634     157.9704            0    3764.0138  0.075484598 
    4100    19458.162    160.55562            0     3763.919    1.7856979 
    4150     19028.89    239.83121            0    3763.6997    11.420854 
    4200    20109.582    39.912078            0    3763.9088   -2.4825779 
    4250    19501.856    151.85318            0     3763.308    4.4374703 
    4300    19953.632     68.83941            0    3763.9565   -1.9144758 
    4350    19109.358    225.03756            0    3763.8075   0.43487388 
    4400    19762.511    104.29295            0    3764.0171    2.7984598 
    4450    19722.718    111.70804            0    3764.0632    2.2845927 
    4500    19915.846    75.911584            0    3764.0312    4.1625614 
    4550    19884.847    81.607953            0     3763.987    2.0252211 
    4600    18612.632    317.21746            0    3764.0011    5.1726513 
    4650    19078.336    230.90268            0    3763.9279     5.205472 
    4700     19715.75    112.95427            0     3764.019    4.3237781 
    4750    19742.684    107.93515            0    3763.9878    2.1485577 
    4800    19197.053    208.91261            0    3763.9225    -2.943785 
    4850    19760.387    104.71117            0    3764.0421   -4.0934577 
    4900     17998.47    431.02848            0    3764.0784    13.811824 
    4950    19604.398    133.53703            0    3763.9811   -5.5636088 
    5000    19232.029    202.51843            0    3764.0053   -1.8269075 
    5050    19715.235    112.97181            0    3763.9412    1.7390053 
    5100    19398.744    171.53062            0    3763.8906    3.3491974 
    5150     19314.84    187.15985            0     3763.982    2.8628327 
    5200    19694.326    116.88381            0    3763.9813   0.87055141 
    5250    19863.902    85.505146            0    3764.0056  -0.59127781 
    5300    18854.279    272.69199            0    3764.2251   0.97585642 
    5350    20102.125    41.375281            0    3763.9911    3.4442258 
    5400    18613.294    317.12781            0    3764.0342    9.5393349 
    5450    19559.083     141.5345            0    3763.5869    3.6962703 
    5500    17569.068    510.18672            0    3763.7179     13.24936 
    5550    19270.914    194.90196            0    3763.5898    3.8986118 
    5600    19498.122    153.15583            0    3763.9191   -3.4776966 
    5650    19777.463    101.36242            0    3763.8555   -11.848632 
    5700    19084.468    229.69625            0    3763.8569    1.2585904 
    5750    18724.734     296.2904            0    3763.8337    2.6582121 
    5800    19386.427    173.81408            0    3763.8932    4.2211994 
    5850    19803.648    96.837994            0    3764.1802    1.3140639 
    5900    19673.781    120.82275            0    3764.1155   -2.5154465 
    5950    19736.953    109.09143            0    3764.0827   -2.2181212 
    6000    19790.274    99.158109            0    3764.0237     -3.68098 
    6050     19545.34    144.53706            0    3764.0444   0.39182955 
    6100    17986.935     433.2002            0     3764.114    10.030916 
    6150    19723.117    111.58597            0     3764.015    2.7481914 
    6200    19196.262     209.2757            0     3764.139   -4.1838898 
    6250    19595.664    135.40327            0    3764.2299   -4.9572417 
    6300    20066.143     48.26479            0    3764.2173   -2.0440702 
    6350    19658.915    123.66551            0    3764.2054    6.3983302 
    6400    16099.375    783.30808            0    3764.6738    10.626182 
    6450    18777.763    287.09552            0    3764.4591    -4.455207 
    6500    16707.737    670.37041            0    3764.3958    13.941367 
    6550    19762.607    104.62762            0    3764.3696   0.16306805 
    6600    19257.046    198.21098            0    3764.3305   -5.4407238 
    6650    19832.195    91.712241            0    3764.3409   -1.9458256 
    6700    19850.998    88.250674            0    3764.3614    5.8183659 
    6750    19413.067    169.26039            0    3764.2728    6.1295075 
    6800    19765.494    103.96165            0    3764.2383   -3.7688435 
    6850    16858.457    642.54223            0    3764.4787    4.5079169 
    6900    19982.921    63.847652            0    3764.3885   -9.1345046 
    6950    19913.352    76.606013            0    3764.2639   -2.5724183 
    7000    19224.043    204.40946            0    3764.4174    8.8267535 
    7050    19611.945    132.75353            0    3764.5952   -1.2121033 
    7100    18439.385    350.13652            0    3764.8375   -10.124288 
    7150    19682.442    120.04202            0    3764.9386   -3.6256683 
    7200    19422.224    168.10408            0    3764.8122   0.82487728 
    7250    18329.588    370.25204            0    3764.6202    11.648525 
    7300     19708.59    114.99145            0    3764.7304  0.046523759 
    7350    19816.323    95.213196            0    3764.9026  -0.47763944 
    7400    17665.439    493.59617            0    3764.9737  -0.91038002 
    7450    19566.729    141.55672            0    3765.0251   -5.4595222 
    7500    19814.753    95.678399            0     3765.077    2.7766353 
    7550    18372.821    362.40112            0    3764.7753    14.250033 
    7600    19501.443    153.75428            0    3765.1326    7.1710143 
    7650    19668.707     122.7639            0     3765.117   -7.9237216 
    7700    19679.165    120.74844            0    3765.0382   -2.2087708 
    7750    19318.592    187.36213            0    3764.8791    5.2470406 
    7800    18421.715    352.99021            0     3764.419    9.1913905 
    7850    18895.708     265.3653            0    3764.5705     5.549395 
    7900     19577.99    139.06024            0     3764.614   -9.4076317 
    7950    19740.609    109.09893            0    3764.7672   -9.8961255 
    8000    18940.832    256.98999            0    3764.5514    3.9687427 
    8050    18969.072    252.07733            0    3764.8685   -4.0865115 
    8100    18105.878    411.85769            0     3764.798    6.9985575 
    8150    17720.026    483.41227            0    3764.8985   -9.9691828 
    8200    19228.141    204.22365            0    3764.9906    4.5129102 
    8250    18208.089    392.95005            0    3764.8183   -1.1095191 
    8300    17975.092    435.94429            0     3764.665    17.753982 
    8350    18763.356    290.24792            0    3764.9434    2.4934075 
    8400    20081.591    46.079041            0    3764.8922   -1.2146918 
    8450    19112.458    225.50295            0     3764.847     -4.35039 
    8500    19307.507     189.3956            0      3764.86    5.0874862 
    8550    19181.088    212.75782            0    3764.8111   0.25341129 
    8600    18801.701     282.9206            0    3764.7171   -11.907333 
    8650    18881.312    268.25685            0    3764.7961    7.0176888 
    8700    15686.277    860.48983            0     3765.356    21.424289 
    8750    18618.866    316.47733            0    3764.4154   -4.6552691 
    8800     18339.56    368.23406            0    3764.4489    2.6401219 
    8850    19445.679    163.71793            0    3764.7697   -2.4895575 
    8900    19121.794     223.5113            0    3764.5842   -5.0630299 
    8950    14402.118    1099.2335            0    3766.2923   -7.4933486 
    9000    19175.071    213.69795            0     3764.637   -5.6657242 
    9050    19412.386    169.60603            0    3764.4924   -12.723782 
    9100    18455.972    346.68851            0    3764.4611    9.1721288 
    9150    19954.848    69.041959            0    3764.3841  -0.91356236 
    9200    19613.768    132.03036            0    3764.2097    4.9013519 
    9250    15254.687    939.82439            0    3764.7665    11.510878 
    9300    19048.696    236.62627            0    3764.1625   0.67464829 
    9350    18952.271     254.3769            0    3764.0568    8.2625973 
    9400    17082.985    600.49483            0    3764.0105   -9.9046787 
    9450    16757.345    660.90075            0    3764.1128    21.116304 
    9500    19841.884    89.284407            0    3763.7073  -0.64193305 
    9550    19304.212    189.00596            0      3763.86   -12.873723 
    9600    16227.696    759.23524            0    3764.3641    11.721944 
    9650    17820.924    463.01451            0    3763.1857    3.9496789 
    9700    19354.393    179.78068            0    3763.9275   -2.6872013 
    9750    13935.985    1183.7739            0    3764.5119    10.647433 
    9800    19587.907    136.31855            0    3763.7087    5.5549859 
    9850    19080.946    230.80379            0    3764.3124   -4.0577518 
    9900    19455.883    161.42232            0    3764.3637   -1.6117009 
    9950    18749.317    292.29982            0    3764.3955    3.9849608 
   10000    18721.798    297.49023            0    3764.4899    1.6710415 
Loop time of 3.82663 on 4 procs for 10000 steps with 81 atoms

Pair  time (%) = 0.0296764 (0.775524)
Neigh time (%) = 0.0208988 (0.546142)
Comm  time (%) = 0.175437 (4.58463)
Outpt time (%) = 0.00546265 (0.142754)
Other time (%) = 3.59515 (93.9509)

Nlocal:    20.25 ave 36 max 0 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Nghost:    16 ave 33 max 2 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs:    162.75 ave 371 max 0 min
Histogram: 2 0 0 0 0 0 0 1 0 1

Total # of neighbors = 651
Ave neighs/atom = 8.03704
Neighbor list builds = 993
Dangerous builds = 949
